Variant report

Variant	rs7638524
Chromosome Location	chr3:52874861-52874862
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52803715..52805902-chr3:52874029..52875964,2	MCF-7	breast:
2	chr3:52864085..52867017-chr3:52872869..52875445,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114904	Chromatin interaction
ENSG00000055955	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12488303	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12496077	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13072536	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13083728	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1573815	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2001735	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2071040	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2071041	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2072391	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2239547	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2276815	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2276817	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2276825	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2336666	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2878762	0.84[ASN][1000 genomes]
rs35004449	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3733047	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3755803	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4302374	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4687554	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4687559	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4687560	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4687657	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4687658	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4687663	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687672	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445538	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445541	0.84[ASN][1000 genomes]
rs6445547	0.86[ASN][1000 genomes]
rs6797399	0.86[ASN][1000 genomes]
rs6798941	0.93[ASN][1000 genomes]
rs7620706	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9682464	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9839035	0.86[ASN][1000 genomes]
rs9876403	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv967253	chr3:52871714-52877079	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3364829	chr3:52874657-52874931	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7638524	ITIH4-AS1	cis	lung	GTEx
rs7638524	MUSTN1	cis	Artery Aorta	GTEx
rs7638524	ITIH4-AS1	cis	Artery Tibial	GTEx
rs7638524	TMEM110	cis	Muscle Skeletal	GTEx
rs7638524	MUSTN1	cis	Thyroid	GTEx
rs7638524	ITIH4-AS1	cis	Whole Blood	GTEx
rs7638524	ITIH4-AS1	cis	Artery Aorta	GTEx
rs7638524	ITIH4	Cis_1M	lymphoblastoid	RTeQTL
rs7638524	SERBP1P3	cis	lung	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52856000-52875000	Weak transcription	Fetal Intestine Large	intestine
3	chr3:52862000-52882600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:52864400-52875800	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr3:52865600-52875200	Weak transcription	Dnd41	blood
6	chr3:52865800-52878600	Weak transcription	Small Intestine	intestine
7	chr3:52866000-52884800	Weak transcription	HMEC	breast
8	chr3:52866200-52885200	Weak transcription	NHEK	skin
9	chr3:52866600-52879200	Weak transcription	Osteobl	bone
10	chr3:52866800-52876400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr3:52866800-52878200	Strong transcription	Fetal Brain Female	brain
12	chr3:52866800-52879600	Genic enhancers	Fetal Thymus	thymus
13	chr3:52867000-52876400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr3:52867000-52881600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:52867000-52881800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:52867200-52875200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:52868000-52878800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:52868000-52883200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:52868400-52877800	Strong transcription	Brain Germinal Matrix	brain
20	chr3:52868600-52875200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:52868800-52876800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:52869000-52878800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:52869000-52879400	Strong transcription	Fetal Intestine Small	intestine
24	chr3:52869000-52881800	Weak transcription	Fetal Kidney	kidney
25	chr3:52869400-52875200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr3:52869400-52875600	Weak transcription	Colonic Mucosa	Colon
27	chr3:52869600-52875000	Strong transcription	Brain Angular Gyrus	brain
28	chr3:52869600-52875200	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr3:52869600-52878600	Weak transcription	NHDF-Ad	bronchial
30	chr3:52869600-52879600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:52869600-52881800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr3:52869800-52875600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:52869800-52876600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:52869800-52882000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr3:52869800-52884000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:52870000-52875000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr3:52870000-52878800	Genic enhancers	Fetal Muscle Leg	muscle
38	chr3:52870000-52901000	Weak transcription	Fetal Brain Male	brain
39	chr3:52870200-52875600	Strong transcription	Stomach Smooth Muscle	stomach
40	chr3:52870200-52876600	Strong transcription	Fetal Stomach	stomach
41	chr3:52870400-52875800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:52870400-52876400	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr3:52870400-52877400	Strong transcription	Lung	lung
44	chr3:52870600-52875000	Weak transcription	Primary B cells from peripheral blood	blood
45	chr3:52870600-52875200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:52870600-52877000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:52870600-52877400	Strong transcription	Adipose Nuclei	Adipose
48	chr3:52870600-52879400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:52871000-52875000	Weak transcription	HSMM	muscle
50	chr3:52871200-52875000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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